seq_id_mapper.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: seq_id_mapper.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 17:27:46  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.23
 * PRODUCTION
 * ===========================================================================
 */

#ifndef OBJECTS_OBJMGR___SEQ_ID_MAPPER__HPP
#define OBJECTS_OBJMGR___SEQ_ID_MAPPER__HPP

/*  $Id: seq_id_mapper.hpp,v 1000.1 2004/04/12 17:27:46 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Aleksey Grichenko, Eugene Vasilchenko
*
* File Description:
*   Seq-id mapper for Object Manager
*
*/

#include <corelib/ncbiobj.hpp>
#include <corelib/ncbi_limits.hpp>
#include <corelib/ncbimtx.hpp>
#include <corelib/ncbicntr.hpp>
#include <corelib/ncbi_safe_static.hpp>

#include <objects/seqloc/Seq_id.hpp>

#include <objmgr/seq_id_handle.hpp>

#include <set>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


class CSeq_id;
class CSeq_id_Which_Tree;


////////////////////////////////////////////////////////////////////
//
//  CSeq_id_Mapper::
//
//    Allows fast convertions between CSeq_id and CSeq_id_Handle,
//    including searching for multiple matches for a given seq-id.
//


typedef set<CSeq_id_Handle>                     TSeq_id_HandleSet;


class NCBI_XOBJMGR_EXPORT CSeq_id_Mapper : public CObject
{
public:
    static CSeq_id_Mapper& GetSeq_id_Mapper(void);
    
    virtual ~CSeq_id_Mapper(void);
    
    // Get seq-id handle. Create new handle if not found and
    // do_not_create is false. Get only the exactly equal seq-id handle.
    CSeq_id_Handle GetGiHandle(int gi);
    CSeq_id_Handle GetHandle(const CSeq_id& id, bool do_not_create = false);

    // Get the list of matching handles, do not create new handles
    bool HaveMatchingHandles(const CSeq_id_Handle& id);
    void GetMatchingHandles(const CSeq_id_Handle& id,
                            TSeq_id_HandleSet& h_set);
    bool HaveReverseMatch(const CSeq_id_Handle& id);
    void GetReverseMatchingHandles(const CSeq_id_Handle& id,
                                   TSeq_id_HandleSet& h_set);
    // Get the list of string-matching handles, do not create new handles
    void GetMatchingHandlesStr(string sid,
                               TSeq_id_HandleSet& h_set);
    
    // Get seq-id for the given handle
    static CConstRef<CSeq_id> GetSeq_id(const CSeq_id_Handle& handle);
    
private:
    CSeq_id_Mapper(void);
    
    friend class CSafeStaticRef<CSeq_id_Mapper>;
    friend class CSeq_id_Handle;
    friend class CSeq_id_Info;

    // References to each handle must be tracked to re-use their values
    // Each CSeq_id_Handle locks itself in the constructor and
    // releases in the destructor.
    bool x_IsBetter(const CSeq_id_Handle& h1, const CSeq_id_Handle& h2);


    CSeq_id_Which_Tree& x_GetTree(const CSeq_id_Handle& idh);
    CSeq_id_Which_Tree& x_GetTree(const CSeq_id& id);

    // Hide copy constructor and operator
    CSeq_id_Mapper(const CSeq_id_Mapper&);
    CSeq_id_Mapper& operator= (const CSeq_id_Mapper&);

    // Some map entries may point to the same subtree (e.g. gb, dbj, emb).
    typedef vector<CRef<CSeq_id_Which_Tree> >                 TTrees;

    TTrees          m_Trees;
    mutable CMutex  m_IdMapMutex;
    
    static CSafeStaticRef<CSeq_id_Mapper> s_Seq_id_Mapper;
};


/////////////////////////////////////////////////////////////////////////////
//
// Inline methods
//
/////////////////////////////////////////////////////////////////////////////


inline
CConstRef<CSeq_id> CSeq_id_Mapper::GetSeq_id(const CSeq_id_Handle& h)
{
    return h.GetSeqId();
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_id_mapper.hpp,v $
* Revision 1000.1  2004/04/12 17:27:46  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.23
*
* Revision 1.23  2004/02/19 17:25:33  vasilche
* Use CRef<> to safely hold pointer to CSeq_id_Info.
* CSeq_id_Info holds pointer to owner CSeq_id_Which_Tree.
* Reduce number of calls to CSeq_id_Handle.GetSeqId().
*
* Revision 1.22  2004/02/10 21:15:14  grichenk
* Added reverse ID matching.
*
* Revision 1.21  2004/01/22 20:10:38  vasilche
* 1. Splitted ID2 specs to two parts.
* ID2 now specifies only protocol.
* Specification of ID2 split data is moved to seqsplit ASN module.
* For now they are still reside in one resulting library as before - libid2.
* As the result split specific headers are now in objects/seqsplit.
* 2. Moved ID2 and ID1 specific code out of object manager.
* Protocol is processed by corresponding readers.
* ID2 split parsing is processed by ncbi_xreader library - used by all readers.
* 3. Updated OBJMGR_LIBS correspondingly.
*
* Revision 1.20  2004/01/07 20:42:00  grichenk
* Fixed matching of accession to accession.version
*
* Revision 1.19  2003/09/30 16:21:59  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.18  2003/06/10 19:06:34  vasilche
* Simplified CSeq_id_Mapper and CSeq_id_Handle.
*
* Revision 1.16  2003/05/20 15:44:37  vasilche
* Fixed interaction of CDataSource and CDataLoader in multithreaded app.
* Fixed some warnings on WorkShop.
* Added workaround for memory leak on WorkShop.
*
* Revision 1.15  2003/04/24 16:12:37  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.14  2003/03/10 16:31:29  vasilche
* Moved implementation constant to .cpp file.
*
* Revision 1.13  2003/02/25 14:48:06  vasilche
* Added Win32 export modifier to object manager classes.
*
* Revision 1.12  2003/01/29 22:03:43  grichenk
* Use single static CSeq_id_Mapper instead of per-OM model.
*
* Revision 1.11  2002/10/03 01:58:27  ucko
* Move the definition of TSeq_id_Info above the declaration of
* CSeq_id_Which_Tree, which uses it.
*
* Revision 1.10  2002/10/02 21:26:53  ivanov
* A CSeq_id_Which_Tree class declaration moved from .cpp to .hpp to make
* KCC happy
*
* Revision 1.9  2002/09/19 20:05:44  vasilche
* Safe initialization of static mutexes
*
* Revision 1.8  2002/07/08 20:51:02  grichenk
* Moved log to the end of file
* Replaced static mutex (in CScope, CDataSource) with the mutex
* pool. Redesigned CDataSource data locking.
*
* Revision 1.7  2002/05/06 03:28:47  vakatov
* OM/OM1 renaming
*
* Revision 1.6  2002/04/22 20:03:48  grichenk
* Redesigned keys usage table to work in 64-bit mode
*
* Revision 1.5  2002/03/15 18:10:09  grichenk
* Removed CRef<CSeq_id> from CSeq_id_Handle, added
* key to seq-id map th CSeq_id_Mapper
*
* Revision 1.4  2002/02/21 19:27:06  grichenk
* Rearranged includes. Added scope history. Added searching for the
* best seq-id match in data sources and scopes. Updated tests.
*
* Revision 1.3  2002/02/12 19:41:42  grichenk
* Seq-id handles lock/unlock moved to CSeq_id_Handle 'ctors.
*
* Revision 1.2  2002/01/23 21:59:32  grichenk
* Redesigned seq-id handles and mapper
*
*
* ===========================================================================
*/

#endif  /* OBJECTS_OBJMGR___SEQ_ID_MAPPER__HPP */